Description Usage Arguments Details Value Author(s) References See Also Examples
This function finds maximum likelihood estimates of hybrid index as described by Buerkle (2005).
1 2 
introgress.data 
a list produced by

loci.data 
a matrix or array providing marker information. 
ind.touse 
vector of individual identifications, numeric indexes,
or logicals that specify a subset of individuals for analysis, if

fixed 
a logical specifying whether different alleles are fixed for each parental population for all markers. 
p1.allele 
if 
p2.allele 
if 
introgress.data
may either be the list that is returned by the
function prepare.data
, or, if fixed=TRUE
,
introgress.data
may simply be a matrix or array providing counts
of the number of alleles derived from parental population 1 for each
admixed individual. If introgress.data
is a matrix or array, rows
and columns correspond to loci and individuals, respectively.
loci.data
is a matrix or array where each row provides
information on one locus. The first column gives a unique locus name
(e.g. "locus3"), and the second column specifies whether the
locus is codominant ("C" or "c"), haploid ("H" or
"h"), or dominant ("D" or "d"). These first two
columns in loci.data
are required. The third column, which is
optional, is a numeric value specifying the linkage groups for the
marker. The fourth column, which is also optional, is a numeric value
specifying both the linkage group and location on the linkage group
(e.g. 3.70, for a marker at 70 cM on linkage group 3). These
optional columns can be used for ordering markers for the
mk.image
, genomic.clines
, and clines.plot
functions.
If the parental populations exhibit fixed allelic differences for all
markers scored (i.e. fixed=TRUE
) then p1.allele
and
p2.allele
should give the character used to specify alleles
derived from parental populations one and two, respectively
(e.g. p1.allele="p1"
and p2.allele="p2"
).
est.h
uses a maximum likelihood method to estimate the hybrid
index for each admixed individual. This estimate is simply the
proportion of alleles derived from population 2 if fixed=TRUE
.
In contrast, if populations share alleles (i.e. fixed=FALSE
), the
estimate accounts for uncertainty in the ancestry of alleles, but the
estimate of hybrid index is still an estimate of the proportion of the
genome that is inherited from population 2. For each individual,
est.h
returns a point estimate and 95% confidence interval of
hybrid index.
See Buerkle (2005) for additional details.
A data frame with point estimates of hybrid index and upper and lower limits of 95% confidence intervals (interval of hybrid index that falls within two support units of the ML estimate):
lower 
Lower limit of 95% confidence interval. 
h 
Maximumlikelihood estimate of hybrid index. 
upper 
Upper limit of 95% confidence interval. 
Zachariah Gompert [email protected], C. Alex Buerkle [email protected]
Buerkle C. A. (2005) Maximumlikelihood estimation of a hybrid index based on molecular markers. Molecular Ecology Notes, 5, 684687.
Gompert Z. and Buerkle C. A. (2009) A powerful regressionbased method for admixture mapping of isolation across the genome of hybrids. Molecular Ecology, 18, 12071224.
Gompert Z. and Buerkle C. A. (2009) introgress: a software package for mapping components of isolation in hybrids. Molecular Ecology Resources, in preparation.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  ## Not run:
## load simulated data
## markers have fixed differences, with
## alleles coded as 'P1' and 'P2'
data(AdmixDataSim1)
data(LociDataSim1)
## use prepare.data to produce introgress.data
introgress.data<prepare.data(admix.gen=AdmixDataSim1,
loci.data=LociDataSim1,
parental1="P1", parental2="P2",
pop.id=FALSE, ind.id=FALSE,
fixed=TRUE)
## estimate hybrid index
hi.index<est.h(introgress.data=introgress.data,
loci.data=LociDataSim1, ind.touse=NULL, fixed=TRUE,
p1.allele="P1", p2.allele="P2")
write.table(hi.index, file="hindex.txt", quote=FALSE, sep=",")
## End(Not run)

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